[gmx-users] center of mass pulling in AFM

Kay Gottschalk kay.gottschalk at physik.uni-muenchen.de
Tue Jul 18 14:41:53 CEST 2006

Ok, that's what we thought. So would you think that it is a better  
idea to fix an atom close to the center of mass instead of the center  
of mass itself? That way, one shouldn't get any additional forces  
acting on the rear end, just forces acting on a single atom in the  
center. Would you agree with that?

On Jul 18, 2006, at 2:16 PM, Berk Hess wrote:

>> From: Kay Gottschalk <kay.gottschalk at physik.uni-muenchen.de>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] center of mass pulling in AFM
>> Date: Tue, 18 Jul 2006 12:44:20 +0200
>> We have a complex with two chains. From one chain (chain A), we  
>> are  fixing the COM. We are pulling on the COM of the other chain  
>> (chain  B). Now assume that due to interactions with chain B,  
>> chain A is  elongated in the direction of pulling. This means that  
>> the COM of  chain A has moved in the directions of chain B. To  
>> keep the COM of  chain A at the same position, the 'rear end' of  
>> chain A has to go in  the opposite direction than the 'front end',  
>> so that chain A  experiences additional forces and is even more  
>> (and now not due to  'real' interactions, but artificially )  
>> elongated due to the COM  fixing. Did I understand that correctly?
> Yes.
> That's a simple question.
> If you keep the COM of a group fixed and part of the group has to
> move in one direction, another part of the group will have to
> move in another direction.
> Berk.
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